|
| Status |
Public on Jul 01, 2012 |
| Title |
mock infected cells |
| Sample type |
SRA |
| |
|
| Source name |
NIH3T3_mock
|
| Organism |
Mus musculus |
| Characteristics |
cell line: NIH3T3
cell type: fibroblasts
infected with: mock (control)
5'-barcode: GAT
|
| Treatment protocol |
Infection with MCMV at MOI of 10, 72 hrs.
For immunoprecipitation, extracts were prepared from cells after 72 h of infection and the proteins were IP'ed with anti-Ago1 (Wako mAB 2A7, cat. no. 015-22411, lot STM2295) or anti-Ago2 (mAB 6F4, a kind gift of G. Meister, antibody published in Zhu et al. J Virol 84, p. 10266 ff), followed by RNA extraction with Trizol.
|
| Growth protocol |
cells were grown in DMEM with 10 % FCS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA with Trizol. Gel purification of small RNAs (17-30nt). 3'- (AMP-5’p=5’pCTGTAGGCACCATCAATdideoxyC-3’) and 5'- (5'-rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrC rUrCrUrUrCrCrGrArUrCrU-3' + 3 nt Barcode (-CUG, -GAU, -CCU)) Adapter ligation, reverse transcription + PCR to append Illumina bridge amplification sequences
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
total RNA, size-selected (17-30 nt)
|
| Data processing |
The sequences in the fastq file were sorted according to the 5'-Barcodes and the barcode was removed. (resulting file: *_no_barcode.fastq, ad-hoc PERL script, available upon request)
The 3'-linker was removed (ad-hoc PERL script, available upon request)
The remaining small RNA sequences were filtered for length between 17 and 23 nucleotides (ad-hoc PERL script, available on request)
sample data table: Sequences were sorted and reduced to a unique set with the LINUX shell commands sort and uniq -c
|
| |
|
| Submission date |
Mar 29, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Klaus Förstemann |
| E-mail(s) |
foerstemann@lmb.uni-muenchen.de
|
| Organization name |
Ludwig-Maximilians University
|
| Department |
Gene Center
|
| Lab |
Förstemann
|
| Street address |
Feodor-Lynen 25
|
| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE36919 |
MCMV infection of cultured mouse cells induces expression of miR-7a. |
|
| Relations |
| SRA |
SRX132070 |
| BioSample |
SAMN00847521 |
